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4dhj

The structure of a ceOTUB1 ubiquitin aldehyde UBC13~Ub complex

Method: X-RAY DIFFRACTION
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Ubiquitin thioesterase otubain-like

Caenorhabditis elegans

UniProt Q9XVR6

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein heterocomplex Heteromer Protein 3 Ubiquitin aldehyde × 1 （P0CG48） Ubiquitin-conjugating enzyme E2 N × 1 （P61088） water × 3 Consistent with protein count
2 Protein heterocomplex Heteromer Protein 3 Ubiquitin aldehyde × 1 （P0CG48） Ubiquitin-conjugating enzyme E2 N × 1 （P61088） water × 3 Consistent with protein count
4 Protein heterocomplex Heteromer Protein 3 Ubiquitin aldehyde × 1 （P0CG48） Ubiquitin-conjugating enzyme E2 N × 1 （P61088） water × 3 Consistent with protein count
5 Protein heterocomplex Heteromer Protein 3 Ubiquitin aldehyde × 1 （P0CG48） Ubiquitin-conjugating enzyme E2 N × 1 （P61088） water × 3 Consistent with protein count

Other States of the Same Protein in the Database

Monomer

None

Homodimer

None

Homotetramer

None

Other homooligomers

None

Heteromeric or nucleic-acid complex
4dhi 4dhj 4dhj 4dhj 4dhj 4dhz 4ldt

7 assemblies

View Construct and Data Evidence
UniProt name OTUBL_CAEEL
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–284； UniProt 1–284 Author chain E； PDBConstruct 1–284； UniProt 1–284 Author chain I； PDBConstruct 1–284； UniProt 1–284 Author chain L； PDBConstruct 1–284； UniProt 1–284

Ubiquitin aldehyde

Homo sapiens

UniProt P0CG48

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein heterocomplex Heteromer Protein 3 Ubiquitin thioesterase otubain-like × 1 （Q9XVR6） Ubiquitin-conjugating enzyme E2 N × 1 （P61088） water × 3 Consistent with protein count
2 Protein heterocomplex Heteromer Protein 3 Ubiquitin thioesterase otubain-like × 1 （Q9XVR6） Ubiquitin-conjugating enzyme E2 N × 1 （P61088） water × 3 Consistent with protein count
3 Protein monomer Monomer Protein 1 water × 1 Consistent with protein count
4 Protein heterocomplex Heteromer Protein 3 Ubiquitin thioesterase otubain-like × 1 （Q9XVR6） Ubiquitin-conjugating enzyme E2 N × 1 （P61088） water × 3 Consistent with protein count
5 Protein heterocomplex Heteromer Protein 3 Ubiquitin thioesterase otubain-like × 1 （Q9XVR6） Ubiquitin-conjugating enzyme E2 N × 1 （P61088） water × 3 Consistent with protein count
6 Protein monomer Monomer Protein 1 No other associated polymer Consistent with protein count

Other States of the Same Protein in the Database

Monomer
1ogw 2l3z 2ld9 2mi8 2mor 2rsu 2ru6 4boz 4dhj 4dhj 4dhz 4hk2

52 assemblies; showing the first 12

Homodimer
2mbo 2mbq 2n2k 3aul 4zqs

5 assemblies

Homotetramer
3alb 8e7o

2 assemblies

Other homooligomers

None

Heteromeric or nucleic-acid complex
11sy 2lvo 2lvp 2lvq 2lz6 2mcn 2mj5 2mre 2mws 2rr9 3b08 3b08

290 assemblies; showing the first 12

View Construct and Data Evidence
UniProt name UBC_HUMAN
Isoform —
PDB entities 2, 3
Chains and sequence ranges Author chain B； PDBConstruct 1–76； UniProt 1–76 Author chain F； PDBConstruct 1–76； UniProt 1–76 Author chain J； PDBConstruct 1–76； UniProt 1–76 Author chain M； PDBConstruct 1–76； UniProt 1–76 Author chain D； PDBConstruct 1–76； UniProt 1–76 Author chain H； PDBConstruct 1–76； UniProt 1–76

Ubiquitin-conjugating enzyme E2 N

Homo sapiens

UniProt P61088

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein heterocomplex Heteromer Protein 3 Ubiquitin thioesterase otubain-like × 1 （Q9XVR6） Ubiquitin aldehyde × 1 （P0CG48） water × 3 Consistent with protein count
2 Protein heterocomplex Heteromer Protein 3 Ubiquitin thioesterase otubain-like × 1 （Q9XVR6） Ubiquitin aldehyde × 1 （P0CG48） water × 3 Consistent with protein count
4 Protein heterocomplex Heteromer Protein 3 Ubiquitin thioesterase otubain-like × 1 （Q9XVR6） Ubiquitin aldehyde × 1 （P0CG48） water × 3 Consistent with protein count
5 Protein heterocomplex Heteromer Protein 3 Ubiquitin thioesterase otubain-like × 1 （Q9XVR6） Ubiquitin aldehyde × 1 （P0CG48） water × 3 Consistent with protein count

Other States of the Same Protein in the Database

Monomer

None

Homodimer

None

Homotetramer

None

Other homooligomers

None

Heteromeric or nucleic-acid complex
1j7d 2c2v 2c2v 3hct 3hcu 3hcu 3von 3von 3von 3von 3von 3von

74 assemblies; showing the first 12

View Construct and Data Evidence
UniProt name UBE2N_HUMAN
Isoform —
PDB entities 4
Chains and sequence ranges Author chain C； PDBConstruct 1–152； UniProt 1–152 Author chain G； PDBConstruct 1–152； UniProt 1–152 Author chain K； PDBConstruct 1–152； UniProt 1–152 Author chain N； PDBConstruct 1–152； UniProt 1–152

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id4dhj
Deposition date deposition_date2012-01-27
Structure title titleThe structure of a ceOTUB1 ubiquitin aldehyde UBC13~Ub complex
Keywords keywordsubiquitination, HYDROLASE-SIGNALING PROTEIN-LIGASE complex; HYDROLASE/SIGNALING PROTEIN/LIGASE
Experimental Method methodX-RAY DIFFRACTION
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3. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

4dhj__assembly_3__model_1

Assembly 3 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

4dhj__assembly_3__model_1 | I(q)

10-2 10-1 104 105 106 q (1/Angstrom) I(q)
100 plotted points; both axes use logarithmic scales.

4dhj__assembly_3__model_1 | P(r) · Pending

The new assembly/model P(r) has not been calculated yet This placeholder does not display legacy data r (Angstrom) P(r)
P(r) will be calculated and displayed separately for the same assembly/model.
Rg（Guinier）12.87 Å
Rg (electron density)11.19 Å
Total Rg12.69 Å
Atom count563
Residues71
Excluded volume10147 ų
Maximum q0.500 Å⁻¹
Assembly Model Structure unit Oligomeric description Status CRYSOL Actions
1 1 4dhj__assembly_1__model_1 trimeric （3） Success 4.1.3-1-20251215 (887e7ef) View Download
2 1 4dhj__assembly_2__model_1 trimeric （3） Success 4.1.3-1-20251215 (887e7ef) View Download
3 1 4dhj__assembly_3__model_1 monomeric （1） Success 4.1.3-1-20251215 (887e7ef) View Download
4 1 4dhj__assembly_4__model_1 trimeric （3） Success 4.1.3-1-20251215 (887e7ef) View Download
5 1 4dhj__assembly_5__model_1 trimeric （3） Success 4.1.3-1-20251215 (887e7ef) View Download
6 1 4dhj__assembly_6__model_1 monomeric （1） Success 4.1.3-1-20251215 (887e7ef) View Download
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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (5)

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6. Fold Classification (SCOP + CATH) 32 domains

SCOP 2.08 (14 domains)

Domain ID domain_idd4dhja_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.3 — Cysteine proteinases
Superfamily Superfamily superfamilyd.3.1 — Cysteine proteinases
Family Family familyd.3.1.0 — automated matches
Domain ID domain_idd4dhjb_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.15 — beta-Grasp (ubiquitin-like)
Superfamily Superfamily superfamilyd.15.1 — Ubiquitin-like
Family Family familyd.15.1.1 — Ubiquitin-related
Domain ID domain_idd4dhjc_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.20 — UBC-like
Superfamily Superfamily superfamilyd.20.1 — UBC-like
Family Family familyd.20.1.1 — UBC-related
Domain ID domain_idd4dhjd_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.15 — beta-Grasp (ubiquitin-like)
Superfamily Superfamily superfamilyd.15.1 — Ubiquitin-like
Family Family familyd.15.1.1 — Ubiquitin-related
Domain ID domain_idd4dhje_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.3 — Cysteine proteinases
Superfamily Superfamily superfamilyd.3.1 — Cysteine proteinases
Family Family familyd.3.1.0 — automated matches
Domain ID domain_idd4dhjf_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.15 — beta-Grasp (ubiquitin-like)
Superfamily Superfamily superfamilyd.15.1 — Ubiquitin-like
Family Family familyd.15.1.1 — Ubiquitin-related
Domain ID domain_idd4dhjg_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.20 — UBC-like
Superfamily Superfamily superfamilyd.20.1 — UBC-like
Family Family familyd.20.1.1 — UBC-related
Domain ID domain_idd4dhjh_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.15 — beta-Grasp (ubiquitin-like)
Superfamily Superfamily superfamilyd.15.1 — Ubiquitin-like
Family Family familyd.15.1.1 — Ubiquitin-related
Domain ID domain_idd4dhji_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.3 — Cysteine proteinases
Superfamily Superfamily superfamilyd.3.1 — Cysteine proteinases
Family Family familyd.3.1.0 — automated matches
Domain ID domain_idd4dhjj_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.15 — beta-Grasp (ubiquitin-like)
Superfamily Superfamily superfamilyd.15.1 — Ubiquitin-like
Family Family familyd.15.1.1 — Ubiquitin-related
Domain ID domain_idd4dhjk_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.20 — UBC-like
Superfamily Superfamily superfamilyd.20.1 — UBC-like
Family Family familyd.20.1.1 — UBC-related
Domain ID domain_idd4dhjl_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.3 — Cysteine proteinases
Superfamily Superfamily superfamilyd.3.1 — Cysteine proteinases
Family Family familyd.3.1.0 — automated matches
Domain ID domain_idd4dhjm_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.15 — beta-Grasp (ubiquitin-like)
Superfamily Superfamily superfamilyd.15.1 — Ubiquitin-like
Family Family familyd.15.1.1 — Ubiquitin-related
Domain ID domain_idd4dhjn_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.20 — UBC-like
Superfamily Superfamily superfamilyd.20.1 — UBC-like
Family Family familyd.20.1.1 — UBC-related

CATH v4.4 (18 domains)

Domain ID domain_id4dhjA01
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology200 — Phosphorylase Kinase; domain 1
Homologous superfamily homologous superfamily60 — Peptidase C65 Otubain, subdomain 1
Domain ID domain_id4dhjA02
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology1300 — 3 helical TM bundles of succinate and fumarate reductases
Homologous superfamily homologous superfamily20 — Peptidase C65 Otubain, subdomain 2
Domain ID domain_id4dhjB00
Class class3 — Alpha Beta
Architecture architecture10 — Roll
Topology topology20 — Ubiquitin-like (UB roll)
Homologous superfamily homologous superfamily90 — Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1
Domain ID domain_id4dhjC00
Class class3 — Alpha Beta
Architecture architecture10 — Roll
Topology topology110 — Ubiquitin Conjugating Enzyme
Homologous superfamily homologous superfamily10 — Ubiquitin Conjugating Enzyme
Domain ID domain_id4dhjD00
Class class3 — Alpha Beta
Architecture architecture10 — Roll
Topology topology20 — Ubiquitin-like (UB roll)
Homologous superfamily homologous superfamily90 — Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1
Domain ID domain_id4dhjE01
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology200 — Phosphorylase Kinase; domain 1
Homologous superfamily homologous superfamily60 — Peptidase C65 Otubain, subdomain 1
Domain ID domain_id4dhjE02
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology1300 — 3 helical TM bundles of succinate and fumarate reductases
Homologous superfamily homologous superfamily20 — Peptidase C65 Otubain, subdomain 2
Domain ID domain_id4dhjF00
Class class3 — Alpha Beta
Architecture architecture10 — Roll
Topology topology20 — Ubiquitin-like (UB roll)
Homologous superfamily homologous superfamily90 — Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1
Domain ID domain_id4dhjG00
Class class3 — Alpha Beta
Architecture architecture10 — Roll
Topology topology110 — Ubiquitin Conjugating Enzyme
Homologous superfamily homologous superfamily10 — Ubiquitin Conjugating Enzyme
Domain ID domain_id4dhjH00
Class class3 — Alpha Beta
Architecture architecture10 — Roll
Topology topology20 — Ubiquitin-like (UB roll)
Homologous superfamily homologous superfamily90 — Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1
Domain ID domain_id4dhjI01
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology200 — Phosphorylase Kinase; domain 1
Homologous superfamily homologous superfamily60 — Peptidase C65 Otubain, subdomain 1
Domain ID domain_id4dhjI02
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology1300 — 3 helical TM bundles of succinate and fumarate reductases
Homologous superfamily homologous superfamily20 — Peptidase C65 Otubain, subdomain 2
Domain ID domain_id4dhjJ00
Class class3 — Alpha Beta
Architecture architecture10 — Roll
Topology topology20 — Ubiquitin-like (UB roll)
Homologous superfamily homologous superfamily90 — Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1
Domain ID domain_id4dhjK00
Class class3 — Alpha Beta
Architecture architecture10 — Roll
Topology topology110 — Ubiquitin Conjugating Enzyme
Homologous superfamily homologous superfamily10 — Ubiquitin Conjugating Enzyme
Domain ID domain_id4dhjL01
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology200 — Phosphorylase Kinase; domain 1
Homologous superfamily homologous superfamily60 — Peptidase C65 Otubain, subdomain 1
Domain ID domain_id4dhjL02
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology1300 — 3 helical TM bundles of succinate and fumarate reductases
Homologous superfamily homologous superfamily20 — Peptidase C65 Otubain, subdomain 2
Domain ID domain_id4dhjM00
Class class3 — Alpha Beta
Architecture architecture10 — Roll
Topology topology20 — Ubiquitin-like (UB roll)
Homologous superfamily homologous superfamily90 — Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1
Domain ID domain_id4dhjN00
Class class3 — Alpha Beta
Architecture architecture10 — Roll
Topology topology110 — Ubiquitin Conjugating Enzyme
Homologous superfamily homologous superfamily10 — Ubiquitin Conjugating Enzyme
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7. Citations (1)